The health benefits associated with polyunsaturated fatty acids [“PUFAs”], especially ω-3 and ω-6 PUFAs, have been well documented. In order to find ways to produce large-scale quantities of ω-3 and ω-6 PUFAs, researchers have directed their work toward the discovery of genes and the understanding of the encoded biosynthetic pathways that result in lipids and fatty acids.
One effort to produce these PUFAs has introduced ω-3/ω-6 PUFA biosynthetic pathways into organisms that do not natively produce ω-3/ω-6 PUFAs. One such organism that has been extensively manipulated is the non-oleaginous yeast, Saccharomyces cerevisiae. However, none of the preliminary results demonstrating limited production of linoleic acid [“LA”], γ-linolenic acid [“GLA”], α-linolenic acid [“ALA”], stearidonic acid [“STA”] and/or eicosapentaenoic acid [“EPA”] are suitable for commercial exploitation.
Other efforts to produce large-scale quantities of ω-3/ω-6 PUFAs have cultivated microbial organisms that natively produce the fatty acid of choice, e.g., heterotrophic diatoms Cyclotella sp. and Nitzschia sp., Pseudomonas, Alteromonas or Shewanella species, filamentous fungi of the genus Pythium, or Mortierella elongata, M. exigua or M. hygrophila. 
All these efforts suffer from an inability to substantially improve the yield of oil or to control the characteristics of the oil composition produced, since the fermentations rely on the natural abilities of the microbes themselves.
Commonly owned U.S. Pat. No. 7,238,482 describes the use of the oleaginous yeast Yarrowia lipolytica as a production host for the production of PUFAs. Oleaginous yeast are defined as those yeast that are naturally capable of oil synthesis and accumulation, where greater than 25% of the cellular dry weight is typical. Optimization of the production host has been described in the art (see for example Int'l App. Pub. No. WO 2006/033723, U.S. Pat. App. Pub. No. 2006-0094092, U.S. Pat. App. Pub. No. 2006-0115881, and U.S. Pat. App. Pub. No. 2006-0110806). The recombinant strains described therein comprise various chimeric genes expressing multiple copies of heterologous desaturases, elongases and acyltransferases and optionally comprise various native desaturase and acyltransferase knockouts to enable PUFA synthesis and accumulation. Further optimization of the host cell is needed for commercial production of PUFAs.
Lin Y. et al suggest that peroxisomes are required for both catabolic and anabolic lipid metabolism (Plant Physiology, 135:814-827 (2004)). However, this hypothesis was based on studies with a homolog of Pex16p in Arabidopsis mutants that had both abnormal peroxisome biogenesis and fatty acid synthesis (i.e., a reduction of oil to approximately 10-16% of wild type in sse1 seeds was reported). Binns, D. et al. (J. Cell Biol., 173(5):719-731 (2006)) also document an intimate collaboration between peroxisomes and lipid bodies in Saccharomyces cerevisiae. But, previous studies of Pex knockouts have not been performed in a PUFA-producing organism.
Applicants have solved the stated problem of optimizing host cells for commercial production of PUFAs by the unpredictable mechanism of disruption of peroxisome biogenesis factor proteins in a PUFA-producing organism, which leads to the unpredictable result of an increase in the amount of PUFAs, as a percent of total fatty acids, in a recombinant PUFA-producing strain of Y. lipolytica. Novel strains containing disruptions in peroxisome biogenesis factor proteins are described herein.